The Arabidopsis embryonic shoot fate map

A cellular platform for the development of synthetic living machines

Robot swarms have, to date, been constructed from artificial materials. Motile biological constructs have been created from muscle cells grown on precisely shaped scaffolds. However, the exploitation of emergent self-organization and functional plasticity into a self-directed living machine has remained a major challenge. We report here a method for generation of in vitro biological robots from frog (Xenopus laevis) cells. These xenobots exhibit coordinated locomotion via cilia present on their surface. These cilia arise through normal tissue patterning and do not require complicated construction methods or genomic editing, making production amenable to high-throughput projects. The biological robots arise by cellular self-organization and do not require scaffolds or microprinting; the amphibian cells are highly amenable to surgical, genetic, chemical, and optical stimulation during the self-assembly process. We show that the xenobots can navigate aqueous environments in diverse ways, heal after damage, and show emergent group behaviors. We constructed a computational model to predict useful collective behaviors that can be elicited from a xenobot swarm. In addition, we provide proof of principle for a writable molecular memory using a photoconvertible protein that can record exposure to a specific wavelength of light. Together, these results introduce a platform that can be used to study many aspects of self-assembly, swarm behavior, and synthetic bioengineering, as well as provide versatile, soft-body living machines for numerous practical applications in biomedicine and the environment.

Clonal sector analysis and cell ablation confirm a function for DORNROESCHEN-LIKE in founder cells and the vasculature in Arabidopsis

Inducible lineage analysis and cell ablation via conditional toxin expression in cells expressing the DORNRÖSCHEN-LIKE transcription factor represent an effective and complementary adjunct to conventional methods of functional gene analysis. Classical methods of functional gene analysis via mutational and expression studies possess inherent limitations, and therefore, the function of a large proportion of transcription factors remains unknown. We have employed two complementary, indirect methods to obtain functional information for the AP2/ERF transcription factor DORNRÖSCHEN-LIKE (DRNL), which is dynamically expressed in flowers and marks lateral organ founder cells. An inducible, two-component Cre-Lox system was used to express beta-glucuronidase GUS in cells expressing DRNL, to perform a sector analysis that reveals lineages of cells that transiently expressed DRNL throughout plant development. In a complementary approach, an inducible system was used to ablate cells expressing DRNL using diphtheria toxin A chain, to visualise the phenotypic consequences. These complementary analyses demonstrate that DRNL functionally marks founder cells of leaves and floral organs. Clonal sectors also included the vasculature of the leaves and petals, implicating a previously unidentified role for DRNL in provasculature development, which was confirmed in cotyledons by closer analysis of drnl mutants. Our findings demonstrate that inducible gene-specific lineage analysis and cell ablation via conditional toxin expression represent an effective and informative adjunct to conventional methods of functional gene analysis.

Ectopic shoot meristem generation in monocotyledonous rpk1 mutants is linked to SAM loss and altered seedling morphology

BACKGROUND

In dicot Arabidopsis thaliana embryos two cotyledons develop largely autonomously from the shoot apical meristem (SAM). Recessive mutations in the Arabidopsis receptor-like kinase RPK1 lead to monocotyledonous seedlings, with low (10 %) penetrance due to complex functional redundancy. In strong rpk1 alleles, about 10 % of these (i. e. 1 % of all homozygotes) did not develop a SAM. We wondered whether RPK1 might also control SAM gene expression and SAM generation in addition to its known stochastic impact on cell division and PINFORMED1 (PIN1) polarity in the epidermis.

RESULTS

SAM-less seedlings developed a simple morphology with a straight and continuous hypocotyl-cotyledon structure lacking a recognizable epicotyl. According to rpk1's auxin-related PIN1 defect, the seedlings displayed defects in the vascular tissue. Surprisingly, SAM-less seedlings variably expressed essential SAM specific genes along the hypocotyl-cotyledon structure up into the cotyledon lamina. Few were even capable of developing an ectopic shoot meristem (eSM) on top of the cotyledon.

CONCLUSIONS

The results highlight the developmental autonomy of the SAM vs. cotyledons and suggest that the primary rpk1 defect does not lie in the seedling's ability to express SAM genes or to develop a shoot meristem. Rather, rpk1's known defects in cell division and auxin homeostasis, by disturbed PIN1 polarity, impact on SAM and organ generation. In early embryo stages this failure generates a simplified monocotyledonous morphology. Once generated, this likely entails a loss of positional information that in turn affects the spatiotemporal development of the SAM. SAM-bearing and SAM-less monocotyledonous phenotypes show morphological similarities either to real monocots or to dicot species, which only develop one cotyledon. The specific cotyledon defect in rpk1 mutants thus sheds light upon the developmental implications of the transition from two cotyledons to one.

Grafting in Arabidopsis

Grafting provides a simple way to generate chimeric plants with regions of different genotypes and thus to assess the cell autonomy of gene action. The technique of grafting has been widely used in other species, but in Arabidopsis, its small size makes the process rather more demanding. However, there are now several well-established grafting procedures available, which we described here, and their use has already contributed greatly to understanding of such processes as shoot branching control, flowering, disease resistance, and systemic silencing.

Mutations in the Arabidopsis RPK1 gene uncouple cotyledon anlagen and primordia by modulating epidermal cell shape and polarity

Plant seedlings have either one or two cotyledons. The mechanisms that regulate this organ number are poorly understood. Mutations in the RECEPTOR-LIKE PROTEIN KINASE1 (RPK1) gene of the dicot Arabidopsis have only one cotyledon, with low penetrance due to complex genetic redundancy. An analysis of patterning genes required for cotyledon initiation showed that these have normal expression patterns, defining the cotyledon anlagen, in rpk1. This was also true for key genes, which organize the shoot apical meristem (SAM). By contrast, epidermal cell shape and polarity were compromised in rpk1 embryos, as evidenced by disturbed polarity of the auxin efflux carrier PIN1. PIN1 is required for the establishment of auxin maxima, which induce and maintain organ primordia. The effects in rpk1 mutants manifest in a spatially and timely stochastic fashion probably due to redundancy of RPK1-like functions. Consistently, auxin maxima showed a stochastic distribution in rpk1 embryos, being at times entirely absent and at other times supernumerary. This variability may explain how monocotyledonous seedlings and cotyledon shape variants can developmentally arise in Arabidopsis and possibly in other plants.

Transcript profiling provides evidence of functional divergence and expression networks among ribosomal protein gene paralogs in Brassica napus

The plant ribosome is composed of 80 distinct ribosomal (r)-proteins. In Arabidopsis thaliana, each r-protein is encoded by two or more highly similar paralogous genes, although only one copy of each r-protein is incorporated into the ribosome. Brassica napus is especially suited to the comparative study of r-protein gene paralogs due to its documented history of genome duplication as well as the recent availability of large EST data sets. We have identified 996 putative r-protein genes spanning 79 distinct r-proteins in B. napus using EST data from 16 tissue collections. A total of 23,408 tissue-specific r-protein ESTs are associated with this gene set. Comparative analysis of the transcript levels for these unigenes reveals that a large fraction of r-protein genes are differentially expressed and that the number of paralogs expressed for each r-protein varies extensively with tissue type in B. napus. In addition, in many cases the paralogous genes for a specific r-protein are not transcribed in concert and have highly contrasting expression patterns among tissues. Thus, each tissue examined has a novel r-protein transcript population. Furthermore, hierarchical clustering reveals that particular paralogs for nonhomologous r-protein genes cluster together, suggesting that r-protein paralog combinations are associated with specific tissues in B. napus and, thus, may contribute to tissue differentiation and/or specialization. Altogether, the data suggest that duplicated r-protein genes undergo functional divergence into highly specialized paralogs and coexpression networks and that, similar to recent reports for yeast, these are likely actively involved in differentiation, development, and/or tissue-specific processes.

Embryogenesis: pattern formation from a single cell

During embryogenesis a single cell gives rise to a functional multicellular organism. In higher plants, as in many other multicellular systems, essential architectural features, such as body axes and major tissue layers are established early in embryogenesis and serve as a positional framework for subsequent pattern elaboration. In Arabidopsis, the apicalbasal axis and the radial pattern of tissues wrapped around it are already recognizable in young embryos of only about a hundred cells in size. This early axial pattern seems to provide a coordinate system for the embryonic initiation of shoot and root. Findings from genetic studies in Arabidopsis are revealing molecular mechanisms underlying the initial establishment of the axial core pattern and its subsequent elaboration into functional shoots and roots. The genetic programs operating in the early embryo organize functional cell patterns rapidly and reproducibly from minimal cell numbers. Understanding their molecular details could therefore greatly expand our ability to generate plant body patterns de novo, with important implications for plant breeding and biotechnology.

CAUT lines: a novel resource for studies of cell autonomy in Arabidopsis

Plant development is critically dependent on the interactions between clonally unrelated cell layers. The cross-talk between layers can be addressed by studies of cell autonomy. Cell autonomy is a property of genetic mosaics composed of cells of differing genotypes. Broadly, if the phenotype of a mutant tissue reflects only its genotype and is unaffected by the presence of wild-type tissue, the trait is cell-autonomous. Conversely, if the phenotype of a mutant tissue reflects that of wild-type tissue in the mosaic, the trait is non-autonomous. Here we report a novel, versatile and robust method for studies of cell autonomy in Arabidopsis. Cell autonomy (CAUT) lines consist of a collection of homozygous stocks, each containing one of 76 mapped T-DNA inserts, each of which corrects the yellow ch-42 mutant to green (CH-42) by complementation. This has the effect of translocating the colour marker to 76 new locations around the genome. X-irradiation of heterozygous CAUT line seeds results in yellow sectors, with loss of the CH-42 transgene and adjacent wild-type genes. This property can be used to remove the wild-type copy of developmental genes in appropriate heterozygotes, resulting in yellow (ch-42) sectors that are hemizygous for the trait of interest. Such sectors can provide insight into cell autonomy. Experiments using the ap1, ap3, ag and clv1 mutants show that CAUT lines are useful in the study of cell autonomy.

Molecular control of stem cell maintenance in shoot apical meristem

Sustained post-embryonic organ initiation and development in plants depends on coordinating the formation and differentiation of pluripotent stem cells in apical meristems. Transcriptional regulation and intercellular signalling appear to play key roles in this coordination process. Here we discuss the current knowledge about the molecular regulation of stem cell maintenance in the shoot apical meristem and recent attempts to delineate the molecular signatures of "stemness" in flowering plants. We also outline contemporary molecular approaches for deciphering the process of stem cell renewal in the shoot apical meristem.

Genomic variability within an organism exposes its cell lineage tree

What is the lineage relation among the cells of an organism? The answer is sought by developmental biology, immunology, stem cell research, brain research, and cancer research, yet complete cell lineage trees have been reconstructed only for simple organisms such as Caenorhabditis elegans. We discovered that somatic mutations accumulated during normal development of a higher organism implicitly encode its entire cell lineage tree with very high precision. Our mathematical analysis of known mutation rates in microsatellites (MSs) shows that the entire cell lineage tree of a human embryo, or a mouse, in which no cell is a descendent of more than 40 divisions, can be reconstructed from information on somatic MS mutations alone with no errors, with probability greater than 99.95%. Analyzing all ~1.5 million MSs of each cell of an organism may not be practical at present, but we also show that in a genetically unstable organism, analyzing only a few hundred MSs may suffice to reconstruct portions of its cell lineage tree. We demonstrate the utility of the approach by reconstructing cell lineage trees from DNA samples of a human cell line displaying MS instability. Our discovery and its associated procedure, which we have automated, may point the way to a future “Human Cell Lineage Project” that would aim to resolve fundamental open questions in biology and medicine by reconstructing ever larger portions of the human cell lineage tree.

The human body is made of about 100 trillion cells, all of which are descendants of a single cell, the fertilized egg. The quest to understand their path of descent, called a cell lineage tree, is shared by many branches of biology and medicine, including developmental biology, immunology, stem cell research, brain research, and cancer research. So far, science has been able to determine the cell lineage tree of tiny organisms only, worms with a thousand cells or so. Our team has discovered that the mutations accumulated in each cell in our body during its normal development from the zygote carry sufficient information to reconstruct, in principle, cell lineage trees for large organisms, including humans. Inspired by this discovery, we developed an automated procedure for the reconstruction of cell lineage trees from DNA samples. A direct application of these results may include the analysis of the development of cancer. The results may also inspire a future “Human Cell Lineage Project,” whose aim would be to reconstruct an entire human cell lineage tree.

The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis

Previously, we identified a novel rice gene, GROWTH-REGULATING FACTOR1 (OsGRF1), which encodes a putative transcription factor that appears to play a regulatory role in stem elongation. We now describe the GRF gene family of Arabidopsis thaliana (AtGRF), which comprises nine members. The deduced AtGRF proteins contain the same characteristic regions--the QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) domains--as do OsGRF1 and related proteins in rice, as well as features indicating a function in transcriptional regulation. Most of the AtGRF genes are strongly expressed in actively growing and developing tissues, such as shoot tips, flower buds, and roots, but weakly in mature stem and leaf tissues. Overexpression of AtGRF1 and AtGRF2 resulted in larger leaves and cotyledons, as well as in delayed bolting of the inflorescence stem when compared to wild-type plants. In contrast, triple insertional null mutants of AtGRF1-AtGRF3 had smaller leaves and cotyledons, whereas single mutants displayed no changes in phenotype and double mutants displayed only minor ones. The alteration of leaf growth in overexpressors and triple mutants was based on an increase or decrease in cell size, respectively. These results indicate that AtGRF proteins play a role in the regulation of cell expansion in leaf and cotyledon tissues.

The polycotyledon mutant of tomato shows enhanced polar auxin transport

The polycotyledon mutant of tomato (Lycopersicon esculentum L. cv Ailsa Craig) showed altered development during embryogenesis and during vegetative and reproductive phases. The phenotype was pleiotropic and included the formation of extra cotyledons, changes in leaf shape, increased number of flowers (indeterminacy) with abnormal floral organs, the formation of epiphyllous structures, and altered gravitropism. The earliest defects were observed at the transition from the globular to the heart stage of embryogenesis with the formation of multiple cotyledons. Epidermal cells in the mutant embryo were smaller and less expanded compared with wild type. Examination of polar auxin transport (PAT) showed a striking enhancement in the case of the mutant. Increase in PAT did not appear to be caused by a decrease in flavonoids because the mutant had normal flavonoid levels. Application of 2,3,5-triiodobenzoic acid, an inhibitor of polar transport of auxin, rescued postgermination phenotypes of young seedlings. Our analysis reveals a level of control that negatively regulates PAT in tomato and its contribution to plant development and organogenesis.

Plant meristems: a merry-go-round of signals

Recent studies have provided significant new insights into the gene actions that specify and maintain stem cells in plant shoots and roots. New layers of genetic control and potential signalling pathways and effector mechanisms have emerged from these new studies and will be reviewed here. These new findings refine the current model in which stem cells in plant meristems are regulated by negative feedback loops and uncover a fundamental mechanism for stem cell maintenance that might be common to shoots and roots.

Molecular genetic analysis of left-right handedness in plants

Handedness in plant growth may be most familiar to us when we think of tendrils or twining plants, which generally form consistent right- or left-handed helices as they climb. The petals of several species are sometimes arranged like fan blades that twist in the same direction. Another less conspicuous example is 'circumnutation', the oscillating growth of axial organs, which alternates between a clockwise and an anti-clockwise direction. To unravel molecular components and cellular determinants of handedness, we screened Arabidopsis thaliana seedlings for helical growth mutants with fixed handedness. Recessive spiral1 and spiral2 mutants show right-handed helical growth in roots, hypocotyls, petioles and petals; semi-dominant lefty1 and lefty2 mutants show opposite left-handed growth in these organs. lefty mutations are epistatic to spiral mutations. Arabidopsis helical growth mutants with fixed handedness may be impaired in certain aspects of cortical microtubule functions, and characterization of the mutated genes should lead us to a better understanding of how microtubules function in left-right handedness in plants.

Transactivation of BARNASE under the AtLTP1 promoter affects the basal pole of the embryo and shoot development of the adult plant in Arabidopsis

Genetically controlled expression of a toxin provides a tool to remove a specific structure and consequently study its role during a developmental process. The availability of many tissue-specific promoters is a good argument for the development of such a strategy in plants. We have developed a conditional system for targeted toxin expression and demonstrated its use for generating embryo phenotypes that can bring valuable information about signalling during embryogenesis. The BARNASE gene was expressed in the Arabidopsis embryo under the control of two promoters, one from the cyclin AtCYCB1 gene and one from the AtLTP1 gene (Lipid Transfer Protein 1). One-hundred percent seed abortion was obtained with the cyclin promoter. Surprisingly however, the embryos displayed a range of lethal phenotypes instead of a single arrested stage as expected from this promoter. We also show that BARNASE expression under the control of the AtLTP1 promoter affects the basal pole of the globular embryo. Together with reporter expression studies, this result suggests a role of the epidermis in controlling the development of the lower tier of the embryo. This defect was not embryo-lethal and we show that the seedlings displayed a severe shoot phenotype correlated to epidermal defects. Therefore, the epidermis does not play an active role during organogenesis in seedlings but is important for the postgermination development of a viable plant.

The SPIRAL genes are required for directional control of cell elongation in Aarabidopsis thaliana

Cells at the elongation zone expand longitudinally to form the straight central axis of plant stems, hypocotyls and roots, and transverse cortical microtubule arrays are generally recognized to be important for the anisotropic growth. Recessive mutations in either of two Arabidopsis thaliana SPIRAL loci, SPR1 or SPR2, reduce anisotropic growth of endodermal and cortical cells in roots and etiolated hypocotyls, and induce right-handed helical growth in epidermal cell files of these organs. spr2 mutants additionally show right-handed twisting in petioles and petals. The spr1spr2 double mutant's phenotype is synergistic, suggesting that SPR1 and SPR2 act on a similar process but in separate pathways in controlling cell elongation. Interestingly, addition of a low dose of either of the microtubule-interacting drugs propyzamide or taxol in the agar medium was found to reduce anisotropic expansion of endodermal and cortical cells at the root elongation zone of wild-type seedlings, resulting in left-handed helical growth. In both spiral mutants, exogenous application of these drugs reverted the direction of the epidermal helix, in a dose-dependent manner, from right-handed to left-handed; propyzamide at 1 microM and taxol at 0.2-0.3 microM effectively suppressed the cell elongation defects of spiral seedlings. The spr1 phenotype is more pronounced at low temperatures and is nearly suppressed at high temperatures. Cortical microtubules in elongating epidermal cells of spr1 roots were arranged in left-handed helical arrays, whereas the highly isotropic cortical cells of etiolated spr1 hypocotyls showed microtubule arrays with irregular orientations. We propose that a microtubule-dependent process and SPR1/SPR2 act antagonistically to control directional cell elongation by preventing elongating cells from potential twisting. Our model may have implicit bearing on the circumnutation mechanism.